LXL04_014682 | RubberDandelionOmics

Gene overview

LXL04_014682

Reference: OH-1004 Chr: Chr03 Coordinates: 54763725-54766621 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1482 bp · LXL04_014682|LXL04_014682|OH1004|cDNA

ATGAAGATGAGCAACATGACAAGTGAAAGCGAGGACAGAATGCAGTCCACTGACTGCATAAATTCACCAAGTGATGAAGCGAGCACTGAAAGAAACATGATGGGAAATGGCACATTGAAGAAAGGTCCATGGACGTCTGCAGAAGATGCAATTCTGATGGAATATGTGAGCAAAAATGGACAGGGGAATTGGAACGCTGTTCAGAAGGACTCTGGGCTTTCACGTTGTGGTAAAAGCTGTCGTTTAAGGTGGGCAAATCA...

CDS

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1482 bp · LXL04_014682|LXL04_014682|OH1004|CDS

ATGAAGATGAGCAACATGACAAGTGAAAGCGAGGACAGAATGCAGTCCACTGACTGCATAAATTCACCAAGTGATGAAGCGAGCACTGAAAGAAACATGATGGGAAATGGCACATTGAAGAAAGGTCCATGGACGTCTGCAGAAGATGCAATTCTGATGGAATATGTGAGCAAAAATGGACAGGGGAATTGGAACGCTGTTCAGAAGGACTCTGGGCTTTCACGTTGTGGTAAAAGCTGTCGTTTAAGGTGGGCAAATCA...

Protein

Download Protein FASTA

493 aa · LXL04_014682|LXL04_014682|OH1004|PROTEIN

MKMSNMTSESEDRMQSTDCINSPSDEASTERNMMGNGTLKKGPWTSAEDAILMEYVSKNGQGNWNAVQKDSGLSRCGKSCRLRWANHLRPDLKKGAFTPEEERRIIELHAKMGNKWARMAIELPGRTDNEIKNFWNTRTKRRQRAGLPIYPPDICLQTLSDNNTQPHPYPNRDTEIIPNNNFQIPGVEFKNFALNQDLLFSQSLLHLPGPTFLDIPTNTLLPQTLGPTSHTNNNFFFPVSQSHPPKRIRRYPIYDGGGGG...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_014682`
TK1151 ID	TkA02G405070
OH-1004 ID	LXL04_014682
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 99.594 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_014682

Location Chr03:54763725-54766621 (-)

Description Similar to GAM1: Transcription factor GAMYB

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g11440`	Transcriptional activator of alpha-amylase expression that binds to 5'-CAACTGTC-3' motif in target gene promoter.	The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development.2005 · DOI: 10.1105/tpc.104.027920 The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis.2010 · DOI: 10.1104/pp.110.160630
`At2g32460`	Transcription activator.	ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination.2007 · DOI: 10.1111/j.1365-313x.2006.02980.x The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis.2010 · DOI: 10.1104/pp.110.160630 MYB97, MYB101 and MYB120 function as male factors that control pollen tube-synergid interaction in Arabidopsis thaliana fertilization.2013 · DOI: 10.1371/journal.pgen.1003933 The over-expression of two transcription factors, ABS5/bHLH30 and ABS7/MYB101, leads to upwardly curly leaves.2014 · DOI: 10.1371/journal.pone.0107637
`At5g06100`	Transcriptional activator of alpha-amylase expression that binds to 5'-CAACTGTC-3' motif in target gene promoter.	The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development.2005 · DOI: 10.1105/tpc.104.027920 ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination.2007 · DOI: 10.1111/j.1365-313x.2006.02980.x The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis.2010 · DOI: 10.1104/pp.110.160630

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2WW87`	Transcriptional activator of gibberellin-dependent alpha-amylase expression in aleurone cells.	No verified direct reference in this release
`Os01g0812000`	Transcriptional activator of gibberellin-dependent alpha- amylase expression in aleurone cells.	Loss-of-function mutations of the rice GAMYB gene impair alpha-amylase expression in aleurone and flower development.2004 · DOI: 10.1105/tpc.017327 Gibberellin modulates anther development in rice via the transcriptional regulation of GAMYB.2009 · DOI: 10.1105/tpc.108.062935 Identification of gamyb-4 and analysis of the regulatory role of GAMYB in rice anther development.2010 · DOI: 10.1111/j.1744-7909.2010.00959.x Convergent starvation signals and hormone crosstalk in regulating nutrient mobilization upon germination in cereals.2012 · DOI: 10.1105/tpc.112.097741

Functional annotation source

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Functional annotation source: OH1004 · LXL04_014682 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0009555 pollen development Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009735 response to cytokinin Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0030154 cell differentiation Biological Process

GO:0043068 positive regulation of programmed cell death Biological Process

KEGG gene cross-reference

ath:AT2G32460

ath:AT3G11440

ath:AT5G06100

dosa:Os01g0812000

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.912

Rank 1 · LXL04_014682 · OH-1004

Cytoplasm0.189

Rank 2 · LXL04_014682 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_014682 · OH-1004

Mitochondrion0.017

Rank 4 · LXL04_014682 · OH-1004

Endoplasmic reticulum0.013

Rank 5 · LXL04_014682 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00249.38Myb_DNA-binding41-88 aa

PF13921.13Myb_DNA-bind_644-104 aa

PF00249.38Myb_DNA-binding94-137 aa

PF13921.13Myb_DNA-bind_697-140 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014682	`PF00249.38`	Myb_DNA-binding	41	88	9.6e-33	112.8
LXL04_014682	`PF13921.13`	Myb_DNA-bind_6	44	104	1.2e-19	70.9
LXL04_014682	`PF00249.38`	Myb_DNA-binding	94	137	9.6e-33	112.8
LXL04_014682	`PF13921.13`	Myb_DNA-bind_6	97	140	1.2e-19	70.9

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FR97`	Arabidopsis thaliana	Transcription factor MYB65	39.558%	Swiss-Prot	moderate database homology
`O80883`	Arabidopsis thaliana	Transcription factor MYB101	73.881%	Swiss-Prot	weak database homology
`Q8W1W6`	Arabidopsis thaliana	Transcription factor MYB33	70.370%	Swiss-Prot	weak database homology
`A2WW87`	Oryza sativa subsp. indica	Transcription factor GAMYB	41.912%	Swiss-Prot	moderate database homology
`Q0JIC2`	Oryza sativa subsp. japonica	Transcription factor GAMYB	41.912%	Swiss-Prot	moderate database homology

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